Module Detail Information

Type: Module
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Description:polydot generates a dotplot for each of an all-against-all comparison of a set of sequences. The dotplots are rendered on a single diagram. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence searching for exact matches between sequence regions ("words"). The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a word from each sequences a dot is plotted. The wordsize is specified by the user. Optionally, information on the sequence and location of all the exact matching regions may be written to file as a feature file. All sequence words of the specified size from the first input sequence are compared with all words from the second input sequence and exact matches identified. A line is plotted on the dotplot corresponding to any exact matching words. Thus any local regions of identity correspond to diagonals in the dotplot.
Input Parameters:
 - Sequences
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Graph Type
 - Graph Prompting
 - Graph Description
 - Graph Title
 - Graph Subtitle
 - Graph X-Axis Title
 - Graph Y-Axis Title
 - Averaging Window
 - Show Common Codon Usage
 - Minimum Value for Common Codon
 - Plot
 - Version
 - Word Size
 - Output Feature Format
 - Features Filename
 - Filename Extension
 - Features Output Directory
 - Base File Name
 - Separate File for Each Entry
Output Parameters:
 - Graph Output File
 - Graph Output Directory
 - Output Directory
 - Output Features
File size:31.8 KB
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